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MOSAIC: A modular single-molecule analysis interface
==================================================================
MOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data. By modeling the nanopore system with an equivalent circuit, MOSAIC leverages the transient response of a molecule entering the channel to quantify pore-molecule interactions. In contrast to existing techniques such as ionic current thresholding or Viterbi decoding, this technique allows the estimation of short-lived transient events that are otherwise not analyzed.
Nanometer-scale pores have demonstrated potential use in biotechnology applications, including DNA sequencing, single-molecule force spectroscopy, and single-molecule mass spectrometry. The data modeling and analysis methods implemented in MOSAIC allow for dramatic improvements in the quantification of molecular interactions with the channel in each of these applications.
**If you use MOSAIC in your work, please cite both papers below:**
1. `Analytical Chemistry 2016, (88) pp. 11900–11907 <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b03725>`_
2. `ACS Nano 2014, (8) pp. 1547–1553. <http://pubs.acs.org/doi/abs/10.1021/nn405761y>`_
Installation
==================================================================
Please refer to the `Installation <https://pages.nist.gov/mosaic/html/doc/GettingStarted.html>`_ section of the MOSAIC documentation for details on installation.
Documentation
==================================================================
A PDF version of the MOSAIC documentation can be downloaded `here <https://github.com/usnistgov/mosaic/raw/nist-pages/latex/MOSAIC.pdf>`_.
Getting Help
==================================================================
If you need help or have questions, please join our mailing list.
To subscribe:
Visit `https://groups.google.com/a/list.nist.gov/group/mosaic/ <https://groups.google.com/a/list.nist.gov/group/mosaic/>`_.
To unsubscribe:
Email `mosaic+unsubscribe@list.nist.gov <mailto:mosaic+unsubscribe@list.nist.gov>`_.
Once subscribed, you can send messages by emailing `mosaic@list.nist.gov <mailto:mosaic@list.nist.gov>`_.
Reporting Problems
==================================================================
Report problems using our `issue tracker <https://github.com/usnistgov/mosaic/issues>`_ on Github.
What's New?
==================================================================
Read the `Change Log <CHANGELOG.rst>`_
Change Log
++++++++++++++++++++++++++++++++++++++++++
**v2.2**
- Updated web UI to allow lowpass filtering (BesselLowpassFilter).
- Allow data source path to be changed from web UI when running in local mode (issue `#109 <https://github.com/usnistgov/mosaic/issues/109>`_).
**v2.1**
- Fixed a bug with dcOffset correction that caused the web UI to not accurately display the trajectory.
- Provide Docker images to allow cross-platfom installs
- Bug fixes
**v2.0**
- Fixed an issue where spurious events were detected that were contained entirely within the open channel current (see `#102 <https://github.com/usnistgov/mosaic/issues/102>`_).
- Changed eval calls to safer `AST <https://docs.python.org/2/library/ast.html>`_-based versions within the core mosaic modules.
- Added detailed Windows build instructions.
**v2.0b1**
- Run MOSAIC using a new web interface.
**v1.3.6**
- Bug Fixes
**v1.3.5**
- Saves raw events in database. Resolves `#93 <https://github.com/usnistgov/mosaic/issues/93>`_.
**v1.3.4**
- Fixed a bug in the default settings that prevented the analysis from starting in some instances.
**v1.3.3**
- Added support for Chimera data files.
- Resolves issues `#92 <https://github.com/usnistgov/mosaic/issues/92>`_ and `#95 <https://github.com/usnistgov/mosaic/issues/95>`_.
**v1.3.2**
- Fixed event partiioning bugs.
- [GUI] UI tweaks.
**v1.3.1**
- Bug fix release.
**v1.3**
- Added a new MOSAIC examples repository that contains plotting scripts and Jupyter notebooks (https://github.com/usnistgov/mosaic-examples)
- Updated Bessel fiter implementation to allow causal and non-causal filters.
- Added the CUSUM+ algorithm (see pull requests #34, #43, #45, and #46)
- Added the ability to read arbitrary binary files.
- Renamed StepResponseAnalysis to ADEPT 2-state.
- Renamed multiStateAnalysis to ADEPT.
- CUSUM+ is now used to generate initial guesses for ADEPT
- Streamlined unit test framework. Added new tests for CUSUM+.
- Updated MOSAIC dependencies to include newer package versions and pandas. Run 'python setup.py mosaic_deps' to update.
- Added a new metadata column (mdStateResTime) that saves the residence time of each state to the database. This affects ADEPT and CUSUM+.
- Processing time per event is now saved to the database.
- Added support for warning status codes that begin with 'w'. These codes preserve metadata in the SQLite output and are used to flag events that need closer inspection.
- Removed mosaicgui from PyPi. 'pip install mosaic-nist' only installs command line modules.
- Top level ConvertTrajIO supports binary and ASCII files.
- Added Travis continous integration support.
- [GUI] Added a binary update service for Windows and OS X.
- [GUI] Added a table that displays fit parameters in the event viewer window.
- [GUI] Added more descriptive fit errors.
- [GUI] Added CUSUM+ support to MOSAIC GUI.
- [GUI] Export SQLITE database to CSV (#56).
- [GUI] Support for warning codes in fit event viewer.
- [GUI] Performance optimizations.
- [GUI] Fit window in MOSAIC GUI displays idealized pulses overlays.
- [GUI] Added additional analysis statistics.
- [Addons] Added CUSUM+ support to Mathematica addon (PlotEvents in MosaicUtils.m)
- [Addons] Mathematica queries are *optionally* handled through an external Python script to improve performance.
- [Addons] Added an option to limit PlotEvents in Mathematica addon to N events.
- Known Issues: See #8, #10, #40, #63 and #69.
**v1.2**
- Added support for arbitrary binary file formats (#33)
- [GUI] Included binary file support.
- Documentation updates and bug fixes.
- *Known Issues:* See #8 and #10.
**v1.1**
- [Addons] IGOR support.
- PyPi package automatically installs MOSAIC dependencies.
- Miscellaneous bug fixes.
- *Known Issues:* See #8 and #10.
**v1.0**
- Fixed a bug in multistate code that constrained the RC constant resulting in systematic fitting errors (pull request #25).
- Updated multistate to include a separate RC constant for each state, to be consistent with functional form in Balijepalli et al., ACS Nano 2014.
- Misc bug fixes in tsvTrajIO parsing.
- The number of states is saved to the MDIO DB for multistate analysis (issue #26).
- Created a new package on PyPI (mosaic-nist) to allow installation with setuptools.
- [GUI] Updated help link to point to Sphinx documentation on Github.
- *Known Issues:* See #8 and #10
**v1.0b3.2**
- [GUI] Misc bug fixes
- [Addons] Added code to import MOSAIC output into Matlab (pull requests #18 and #20)
- [Addons] Updated Mathematica addons to automatically decode multi-state data.
- Resolves issues #16 and #22
**v1.0b3.1**
- [GUI] Added multiState support to mosaicgui.
- Analysis information such as alogirthms used, data type, etc. are now stored within a MDIO database.
- [GUI] Autocomplete in mosaicgui only suggests database columns that are valid when used in a query.
- Reorganized Mathematica addon code.
**v1.0b3**
- Fixed a bug that prevented events longer than ~700 data points from being correctly analyzed.
- Fixed a problem that prevented event data from being correctly padded before analysis.
- Resolves #2. TrajIO settings are now read in from the settings file.
- [GUI] Resolves #3. Threshold entry box in GUI becomes nonresponsive when meanOpenCurr is negative.
- [GUI] Resolves #4. Analysis fails when using wavletDenioseFilter from GUI.
- [GUI] Histogram in BlockDepthViewer window can be saved to a CSV file from the File Menu.
- Analysis log is saved to the MDIO database.
- [GUI] ConsoleLogViwer displays the analysis log saved in the MDIO database.
- [GUI] Added a new dialog that displays an experimental feature warning wavelet-based denoising is selected.
- Updated error codes reported in database to be more descriptive of the failure.
- Improved and expanded unit testing framework.
- Moved installation and testing to setuptools.
**v1.0b2**
- [GUI] Fixed threshold update error from 1.0b1.
- Considerably improved automatic open channel state detection.
- The default settings string is now included within the source code.
- Implemented new top-level class ConvertToCSV that allows conversion of data read by any TrajIO object to comma separated files.
- Updated build system and unit testing framework.
- [GUI] Misc UI updates.
**v1.0b1**
- [GUI] Added a menu option to save a settings file prior to starting the analysis.
- [GUI] Current threshold is now defined by an ionic current. The trajectory viewer displays the deviation of the threshold from the mean current.
- Analysis settings are saved within the analysissettings table of the sqlite database. When an analysis database is loaded into the GUI, settings are parsed from within the database.
- When an analysis file is loaded, widgets in the main window remain enabled. This allows starting a new analysis run with the current settings.
- [GUI] Implemented an analysis log viewer that displays the event processing log.
- [GUI] Initial commit of wavelets based peak detection in blockdepthview.
- [GUI] Added all points histogram to trajectory viewer.
- *Known Issues:* Selecting automatic baseline detection can sometimes cause the threshold in the trajectory viewer to change. Moving the slider will cause the settings and trajectory windows to synchronize.
Raw data
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"description": ".. image:: https://img.shields.io/travis/usnistgov/mosaic/master.svg?label=linux\n\t\t:target: https://travis-ci.org/usnistgov/mosaic\n.. image:: https://img.shields.io/travis/usnistgov/mosaic/master.svg?label=macOS\n\t\t:target: https://travis-ci.org/usnistgov/mosaic\n.. image:: https://img.shields.io/github/v/release/usnistgov/mosaic\n\t\t:target: https://github.com/usnistgov/mosaic\n.. image:: https://img.shields.io/pypi/v/mosaic-nist.svg\n\t:target: https://pypi.org/project/mosaic-nist/\n.. image:: https://codecov.io/gh/usnistgov/mosaic/branch/master/graph/badge.svg\n\t:target: https://codecov.io/gh/usnistgov/mosaic \n.. image:: https://img.shields.io/badge/dev-NIST-blue\n\t:target: https://www.nist.gov\n\t\nMOSAIC: A modular single-molecule analysis interface\n==================================================================\n\nMOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data. By modeling the nanopore system with an equivalent circuit, MOSAIC leverages the transient response of a molecule entering the channel to quantify pore-molecule interactions. In contrast to existing techniques such as ionic current thresholding or Viterbi decoding, this technique allows the estimation of short-lived transient events that are otherwise not analyzed.\n\nNanometer-scale pores have demonstrated potential use in biotechnology applications, including DNA sequencing, single-molecule force spectroscopy, and single-molecule mass spectrometry. The data modeling and analysis methods implemented in MOSAIC allow for dramatic improvements in the quantification of molecular interactions with the channel in each of these applications.\n\n**If you use MOSAIC in your work, please cite both papers below:**\n\n1. `Analytical Chemistry 2016, (88) pp. 11900\u201311907 <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b03725>`_\n2. `ACS Nano 2014, (8) pp. 1547\u20131553. <http://pubs.acs.org/doi/abs/10.1021/nn405761y>`_\n\nInstallation\n==================================================================\n\nPlease refer to the `Installation <https://pages.nist.gov/mosaic/html/doc/GettingStarted.html>`_ section of the MOSAIC documentation for details on installation.\n\nDocumentation\n==================================================================\n\nA PDF version of the MOSAIC documentation can be downloaded `here <https://github.com/usnistgov/mosaic/raw/nist-pages/latex/MOSAIC.pdf>`_.\n\nGetting Help\n==================================================================\n\nIf you need help or have questions, please join our mailing list.\n\nTo subscribe:\n\n\tVisit `https://groups.google.com/a/list.nist.gov/group/mosaic/ <https://groups.google.com/a/list.nist.gov/group/mosaic/>`_.\n\nTo unsubscribe:\n\n\tEmail `mosaic+unsubscribe@list.nist.gov <mailto:mosaic+unsubscribe@list.nist.gov>`_.\n\nOnce subscribed, you can send messages by emailing `mosaic@list.nist.gov <mailto:mosaic@list.nist.gov>`_.\n\nReporting Problems\n==================================================================\n\nReport problems using our `issue tracker <https://github.com/usnistgov/mosaic/issues>`_ on Github.\n\nWhat's New?\n==================================================================\n\nRead the `Change Log <CHANGELOG.rst>`_\n\nChange Log\n++++++++++++++++++++++++++++++++++++++++++\n\n**v2.2**\n\n- Updated web UI to allow lowpass filtering (BesselLowpassFilter).\n- Allow data source path to be changed from web UI when running in local mode (issue `#109 <https://github.com/usnistgov/mosaic/issues/109>`_).\n\n**v2.1**\n\n- Fixed a bug with dcOffset correction that caused the web UI to not accurately display the trajectory.\n- Provide Docker images to allow cross-platfom installs\n- Bug fixes\n\n**v2.0**\n\n- Fixed an issue where spurious events were detected that were contained entirely within the open channel current (see `#102 <https://github.com/usnistgov/mosaic/issues/102>`_).\n- Changed eval calls to safer `AST <https://docs.python.org/2/library/ast.html>`_-based versions within the core mosaic modules.\n- Added detailed Windows build instructions.\n\n**v2.0b1**\n\n- Run MOSAIC using a new web interface.\n\n**v1.3.6**\n\n- Bug Fixes\n\n**v1.3.5**\n\n- Saves raw events in database. Resolves `#93 <https://github.com/usnistgov/mosaic/issues/93>`_.\n\n**v1.3.4**\n\n- Fixed a bug in the default settings that prevented the analysis from starting in some instances.\n\n**v1.3.3**\n\n- Added support for Chimera data files.\n- Resolves issues `#92 <https://github.com/usnistgov/mosaic/issues/92>`_ and `#95 <https://github.com/usnistgov/mosaic/issues/95>`_.\n\n**v1.3.2**\n\n- Fixed event partiioning bugs.\n- [GUI] UI tweaks.\n\n**v1.3.1**\n\n- Bug fix release.\n\n**v1.3**\n\n- Added a new MOSAIC examples repository that contains plotting scripts and Jupyter notebooks (https://github.com/usnistgov/mosaic-examples)\n\n- Updated Bessel fiter implementation to allow causal and non-causal filters.\n- Added the CUSUM+ algorithm (see pull requests #34, #43, #45, and #46)\n- Added the ability to read arbitrary binary files.\n- Renamed StepResponseAnalysis to ADEPT 2-state.\n- Renamed multiStateAnalysis to ADEPT.\n- CUSUM+ is now used to generate initial guesses for ADEPT\n- Streamlined unit test framework. Added new tests for CUSUM+.\n- Updated MOSAIC dependencies to include newer package versions and pandas. Run 'python setup.py mosaic_deps' to update.\n- Added a new metadata column (mdStateResTime) that saves the residence time of each state to the database. This affects ADEPT and CUSUM+.\n- Processing time per event is now saved to the database.\n- Added support for warning status codes that begin with 'w'. These codes preserve metadata in the SQLite output and are used to flag events that need closer inspection.\n- Removed mosaicgui from PyPi. 'pip install mosaic-nist' only installs command line modules. \n- Top level ConvertTrajIO supports binary and ASCII files.\n- Added Travis continous integration support.\n- [GUI] Added a binary update service for Windows and OS X.\n- [GUI] Added a table that displays fit parameters in the event viewer window.\n- [GUI] Added more descriptive fit errors.\n- [GUI] Added CUSUM+ support to MOSAIC GUI.\n- [GUI] Export SQLITE database to CSV (#56).\n- [GUI] Support for warning codes in fit event viewer.\n- [GUI] Performance optimizations.\n- [GUI] Fit window in MOSAIC GUI displays idealized pulses overlays.\n- [GUI] Added additional analysis statistics.\n\n- [Addons] Added CUSUM+ support to Mathematica addon (PlotEvents in MosaicUtils.m)\n- [Addons] Mathematica queries are *optionally* handled through an external Python script to improve performance.\n- [Addons] Added an option to limit PlotEvents in Mathematica addon to N events.\n\n- Known Issues: See #8, #10, #40, #63 and #69.\n\n**v1.2**\n\n- Added support for arbitrary binary file formats (#33)\n- [GUI] Included binary file support.\n- Documentation updates and bug fixes.\n- *Known Issues:* See #8 and #10.\n\n**v1.1**\n\n- [Addons] IGOR support.\n- PyPi package automatically installs MOSAIC dependencies.\n- Miscellaneous bug fixes.\n- *Known Issues:* See #8 and #10.\n\n**v1.0**\n\n- Fixed a bug in multistate code that constrained the RC constant resulting in systematic fitting errors (pull request #25).\n- Updated multistate to include a separate RC constant for each state, to be consistent with functional form in Balijepalli et al., ACS Nano 2014.\n- Misc bug fixes in tsvTrajIO parsing.\n- The number of states is saved to the MDIO DB for multistate analysis (issue #26).\n- Created a new package on PyPI (mosaic-nist) to allow installation with setuptools.\n- [GUI] Updated help link to point to Sphinx documentation on Github.\n- *Known Issues:* See #8 and #10 \n\n**v1.0b3.2**\n\n- [GUI] Misc bug fixes\n- [Addons] Added code to import MOSAIC output into Matlab (pull requests #18 and #20)\n- [Addons] Updated Mathematica addons to automatically decode multi-state data.\n- Resolves issues #16 and #22\n\n**v1.0b3.1**\n\n- [GUI] Added multiState support to mosaicgui.\n- Analysis information such as alogirthms used, data type, etc. are now stored within a MDIO database.\n- [GUI] Autocomplete in mosaicgui only suggests database columns that are valid when used in a query.\n- Reorganized Mathematica addon code.\n\n\n**v1.0b3**\n\n- Fixed a bug that prevented events longer than ~700 data points from being correctly analyzed.\n- Fixed a problem that prevented event data from being correctly padded before analysis.\n- Resolves #2. 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